Draft genome sequences of Mycobacterium caprae strains linked to human tuberculosis in Canada

TL;DR

This paper presents draft genome sequences of two Mycobacterium caprae strains linked to human tuberculosis in Canada.

Contribution

The study provides new draft genome sequences of M. caprae strains, which could aid in understanding their spread and improving diagnostics.

Findings

The draft genomes of two M. caprae strains were sequenced.

These genomes may enhance understanding of M. caprae epidemiology and diagnostic development.

Abstract

Mycobacterium caprae is a causative agent of tuberculosis that affects both humans and animals. Here, we present the draft genome sequences of two M. caprae strains. These genome sequences may improve understanding of M. caprae epidemiology and support diagnostic development.

Tables

TABLE 1. Genomic features of the Mycobacterium caprae strains

Strain name	No. of reads	Coverage (×)	Assembly size (bp)	N50 (bp)	No. of contigs	No. of CDSsa	No. of genes	No. of rRNAs	No. of tRNAs	Genome completeness (%) - CheckM	Genome contamination (%) - CheckM	Genome accession no.
300103	1,514,982	68.05	4,347,424	136,136	79	4,101	4,152	3	45	95.25	0.37	JBKGTX000000000
800347	2,870,356	179.55	4,311,143	104,531	111	4,102	4,153	3	45	94.73	0.37	JBLBUU000000000

Full text

ANNOUNCEMENT

Mycobacterium caprae, first proposed as M. tuberculosis subsp. caprae in 1999 (1) and later elevated to the species rank (2), causes tuberculosis in livestock, wildlife animals, and humans (3–7). M. caprae has been described as the animal-adapted lineage “La2” by recent nomenclature (8). Presently, a small number of human-originated M. caprae genome sequences are available, and thus, the epidemiology of this organism is still poorly understood. In the present study, two clinical M. caprae strains 300103 and 800347 were isolated from peritoneal fluid and sputum samples of patients who were sick with tuberculosis in the Canadian provinces of Quebec in 2002 and Alberta in 2008, respectively. The provincial laboratories grew the original cultures 300103 and 800347 aerobically at 37°C onto Löwenstein-Jensen slant for 2 weeks and in BACTEC tube in the BD BACTEC 460 System for a week, respectively. The cultures were forwarded to the National Reference Centre for Mycobacteriology for identification. The identification was confirmed by the presence of a special combination of pncA, katG, and gyrA gene mutations as described by Aranaz et al. (2) and other unique mutations in the gyrB (2, 9) and LeuS genes (9) specific to M. caprae. Phenotypic drug susceptibility testing (DST) for the first-line drugs (i.e*.,* isoniazid, rifampicin, ethambutol, and pyrazinamide) was performed using the BACTEC 460 System. Genomic DNA was extracted using the InstaGene Matrix (9) comprising 6% (w/v) Chelex resin for PCR-ready DNA purification (Bio-Rad#7326030; California, United States) and sequenced using an Illumina MiSeq platform (Illumina Inc.), with the Illumina DNA Prep Kit to generate 2 × 150 bp. Raw sequencing reads were quality checked using FastQC (10) and SMALT (https://www.sanger.ac.uk/tool/smalt-0/) in a Galaxy (11) workflow. The reads were processed in the IRIDA (12) by Shovill v.1.0.4, which used SPAdes v.3.14.1 for de novo assembly (13) and QUAST for assembly assessment (14). The genome annotation was carried out by the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline 2024-07-18.build7555 (15). CheckM v.1.2.3, incorporated in the PGAP, was used to assess the quality of the genomes. Mykrobe v.0.10.0 (16) and TBProfiler v.6.4.0 (17) were employed for predicting antimicrobial resistance. Default parameters were used for all software unless otherwise mentioned.

The assembly and annotations statistics are shown in Table 1. The genomes of M. caprae strains 300103 and 800347 contain 4,101 and 4,102 predicted coding DNA sequences, respectively, with a high G+C content (65.5%). Each strain has 45 tRNAs and three complete rRNAs (one copy of each 5S, 16S, and 23S). FastANI (v1.33) (18) whole-genome comparison of 300103 and 800347 with a reference M. caprae ATCC BAA-824 (2, 19) generated an average nucleotide identity of 99.93% and 99.94%, respectively. The strains were predicted to be fully susceptible to pyrazinamide, isoniazid, rifampicin, and ethambutol. These results were concordant with phenotypic DST.